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2-ethoxy-3,4-dihydro-2h-pyran in complex with T4 lysozyme L99A/M102Q
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LGU PDB ENTRY 1LGU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 6.5, vapor diffusion, hanging drop, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.7 54.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.11 α = 90 b = 60.11 β = 90 c = 96.44 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 296 CCD ADSC QUANTUM 315r 2008-01-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11589 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.25 30 95.3 0.065 15.46 6.29 53814 53814
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.25 1.33 76.7 0.257 4.8 4.93
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION REFMAC THROUGHOUT PDB ENTRY 1LGU 1.26 27.35 53812 52735 1077 100 0.16483 0.1645 0.1637 0.18101 0.1789 RANDOM 12.662
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.22 0.11 0.22 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.026 r_dihedral_angle_3_deg 10.69 r_dihedral_angle_4_deg 10.309 r_dihedral_angle_1_deg 4.704 r_sphericity_free 3.095 r_sphericity_bonded 2.388 r_scangle_it 2.262 r_scbond_it 1.705 r_mcangle_it 1.204 r_angle_refined_deg 1.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.026 r_dihedral_angle_3_deg 10.69 r_dihedral_angle_4_deg 10.309 r_dihedral_angle_1_deg 4.704 r_sphericity_free 3.095 r_sphericity_bonded 2.388 r_scangle_it 2.262 r_scbond_it 1.705 r_mcangle_it 1.204 r_angle_refined_deg 1.168 r_rigid_bond_restr 0.917 r_mcbond_it 0.81 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.205 r_nbd_refined 0.191 r_xyhbond_nbd_refined 0.16 r_symmetry_hbond_refined 0.134 r_chiral_restr 0.08 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1375 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 18
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction ADSC data collection XDS data reduction XDS data scaling REFMAC phasing